agentmods.dev

scgpt

scgpt is a skill for Claude Code, Codex from JimLiu/science-skills. It costs 89 tokens per session (1,399 once invoked), scanned A, original, no licence file.

A toolkit for representing and annotating single-cell gene-expression data with scGPT, a model trained on single-cell biology data.

In plain words
What is it for?
Creating cell embeddings for clustering or integration, assigning cell types without examples, fine-tuning annotations, and producing gene representations for perturbation or gene-regulation studies.
Why use it?
It helps turn gene-expression measurements into useful cell representations and assign cell types when labels are missing or incomplete.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

not rated 229repo +1 changed 8d ago A scan 89 tokens no licence

Good fit Creating cell embeddings for clustering or integration, assigning cell types without examples, fine-tuning annotations, and producing gene representations for perturbation or gene-regulation studies.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jimliu/science-skills/scgpt
View source ↗ JimLiu/science-skills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add JimLiu/science-skills --skill scgpt
Clone the repo
git clone --depth 1 https://github.com/JimLiu/science-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for scgpt

README.md
[![agentmods](https://agentmods.dev/badge/skills/jimliu/science-skills/scgpt/github.svg)](https://agentmods.dev/skills/jimliu/science-skills/scgpt)
Your own site
<a href="https://agentmods.dev/skills/jimliu/science-skills/scgpt"><img src="https://agentmods.dev/badge/skills/jimliu/science-skills/scgpt/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for scgpt

Your own site · 80×15
<a href="https://agentmods.dev/skills/jimliu/science-skills/scgpt"><img src="https://agentmods.dev/badge/skills/jimliu/science-skills/scgpt.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 89 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,399 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00089 $0.01399
Opus 5.5 $0.00036 $0.00560
Sonnet 5.5 $0.00018 $0.00280
Haiku 4.5 $0.00009 $0.00140

Measured 8d ago against content hash cfc7161b3dcc, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

scgpt scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/scgpt/SKILL.md · 151 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 8d ago Changed · +1 lines cfc7161b3dcc
  2. 2mo ago First seen · 150 lines · 89 tokens per session scan A 7af27c91d22a

Subscribe to this mod's changes

scgpt is a skill published in the GitHub repository JimLiu/science-skills (229 stars, last pushed 8d ago), with no licence file. It adds 89 tokens to every session and 1,399 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Data and AIScientificbiomodels
Related

scgpt compared with skills from other repositories

scgpt next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
scgptJimLiu/science-skillsSkill2298d agononeA89Claude Code, Codex
esmfold2aipoch/open-scienceSkill5.5kyesterdayApache-2.0A223Claude Code, Codex
evo2aipoch/open-scienceSkill5.5kyesterdayApache-2.0A83Claude Code, Codex
scgptaipoch/open-scienceSkill5.5kyesterdayApache-2.0A89Claude Code, Codex
esmfold2HughYau/AcademicForgeSkill2.6k5d agononeA223Claude Code, Codex
boltzHughYau/AcademicForgeSkill2.6k5d agononeA88Claude Code, Codex
evo2HughYau/AcademicForgeSkill2.6k5d agononeA83Claude Code, Codex